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August 2026


Malay. J. Biochem. Mol. Biol. (2026) 29 (2)

Page range 1-58

Regular Article 

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DOI:

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Page 1-9

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Zaleha Md Toha, Nor Hasyimah Haron, Nik Nur Syazni, Melati Khairuddean and Hasni Arsad

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HIGH-QUALITY RNA-SEQ DATA OF HUMAN BREAST CANCER CELLS TREATED

WITH Clinacanthus nutans LEAF DICHLOROMETHANE EXTRACTS

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Abstract 

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Clinacanthus nutans (C. nutans) is traditionally used as a medicinal plant for the treatment of breast cancer, yet studies at the RNA molecular level remain limited, particularly regarding RNA stability and quality. This study evaluated the quality of RNA sequencing (RNA-Seq) data obtained from human breast cancer cells (MCF-7) treated with dichloromethane leaf extract of C. nutans, focusing on RNA extraction and determining whether the RNA quality, integrity and quantity met the requirements for downstream RNA-Seq analysis. The RNA purity was confirmed by an A260/280 ratio ranging from 2.0 to 2.2, while all samples showed RNA Integrity Number (RIN) values ≥8, meeting the recommended benchmark for RNA-Seq. Although the 28S/18S ratio was below 2, it remained within the acceptable range. RNA concentration was generally higher in untreated samples compared to controls, as measured using NanoDrop and Bioanalyzer. RNA-Seq generated an average of 52 million paired-end reads per sample and the raw reads passed all quality control parameters, showing uniform read lengths of 151 bp, 100% base coverage, 54% GC content and a base quality score of 36. Analysis of highly expressed genes in treated MCF-7 cells further indicated that the sequencing reads accurately reflected the transcriptome of cells exposed to the dichloromethane C. nutans extract. Overall, the results demonstrate that high-quality RNA and sequencing data were successfully obtained, supporting the application of RNA-Seq to investigate transcriptomic changes induced by C.nutans in breast cancer cells.

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